C o p y r i g h t b y Q u i n t e s s e n z Alle Rechte vorbehalten ENDO (Lond Engl) 2008;2(1)7-20  7 REVIEW The unequivocal role of microorganisms in the aetiology of apical periodontitis has been well estab- lished. As a consequence, successful treatment of this disease is contingent upon effective elimination or maximal reduction of the involved microbiota. There are at least two major aspects of endodontic infection that need to be well understood for establishing effective therapeutic protocols: the compo- sition of the endodontic microbiota associated with the different forms of apical periodontitis and dif- ferent types of infection (i.e. which are the main candidate pathogens); and the patterns of microbial colonisation within the root canal system (i.e. how they are distributed along the infected tissues). This review focuses on the current knowledge of these two aspects. Proper interpretation and clinical appli- cation of this information has the potential to be translated into improvements in quality and pre- dictability of the treatment offered to patients. José F Siqueira Jr, Isabela N Rôças Update on endodontic microbiology: candidate pathogens and patterns of colonisation apical periodontitis, endodontic infection, endodontic pathogens, root canal treatment Key words José F Siqueira Jr Department of Endodontics, School of Dentistry, Estácio de Sá University, Av. Alfredo Baltazar da Silveira, 580/cobertura, Recreio, Rio de Janeiro, RJ, Brazil 22790-701 Tel: +55 21 8874 1022 Fax: +55 21 2199 2204 Email: jf_siqueira@yahoo.com; siqueira@estacio.br Isabela N Rôças Department of Endodontics, School of Dentistry, Estácio de Sá University, Rio de Janeiro, RJ, Brazil This review was invited by the editors of ENDO.  Introduction Endodontic infection is the infection of the root canal system and is the major aetiological agent of apical periodontitis 1,2 . Although fungi, and most recently archaea and viruses, have been found in association with endodontic infection 3-6 , bacteria are the major microorganisms implicated in the pathogenesis of apical periodontitis. The endodontic infectious process usually takes place following pulp necrosis as a result of caries, trauma or iatrogenic procedures. The root canal con- taining a necrotic pulp then affords microorganisms a moist, warm, nutritious and anaerobic environment, which is by and large protected from the host defences. Such conditions are highly propitious for the establishment of a mixed microbiota conspicuously dominated by anaerobic bacterial species 7 , most of which are usually normal inhabitants of the oral cavity. Therefore, endodontic infection is regarded as endoge- nous infection. In advanced stages of the infectious process, bacterial organisations resembling biofilms can be observed adhered to the canal walls 8-10 . Thus, there is a current trend to include apical periodontitis in the category of biofilm-induced diseases (for a review on endodontic biofilms, see Ozok et al 11 ).